skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on November 28, 2020

Title: RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Authors:
ORCiD logo [1]; ORCiD logo [2];  [2]; ORCiD logo [3];  [2];  [2];  [3];  [2];  [2]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [4]
  1. Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New Jersey Piscataway New Jersey, Institute for Quantitative Biomedicine, RutgersThe State University of New Jersey Piscataway New Jersey, The Scripps Research Institute La Jolla California
  2. Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New Jersey Piscataway New Jersey, Institute for Quantitative Biomedicine, RutgersThe State University of New Jersey Piscataway New Jersey
  3. Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of California San Diego California
  4. Research Collaboratory for Structural Bioinformatics Protein Data Bank, RutgersThe State University of New Jersey Piscataway New Jersey, Institute for Quantitative Biomedicine, RutgersThe State University of New Jersey Piscataway New Jersey, Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of California San Diego California, Rutgers Cancer Institute of New Jersey, RutgersThe State University of New Jersey New Brunswick New Jersey
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1576653
Grant/Contract Number:  
DE‐SC0019749
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Protein Science
Additional Journal Information:
Journal Name: Protein Science; Journal ID: ISSN 0961-8368
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Goodsell, David S., Zardecki, Christine, Di Costanzo, Luigi, Duarte, Jose M., Hudson, Brian P., Persikova, Irina, Segura, Joan, Shao, Chenghua, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., and Burley, Stephen K. RCSB Protein Data Bank: Enabling biomedical research and drug discovery. United Kingdom: N. p., 2019. Web. doi:10.1002/pro.3730.
Goodsell, David S., Zardecki, Christine, Di Costanzo, Luigi, Duarte, Jose M., Hudson, Brian P., Persikova, Irina, Segura, Joan, Shao, Chenghua, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., & Burley, Stephen K. RCSB Protein Data Bank: Enabling biomedical research and drug discovery. United Kingdom. doi:10.1002/pro.3730.
Goodsell, David S., Zardecki, Christine, Di Costanzo, Luigi, Duarte, Jose M., Hudson, Brian P., Persikova, Irina, Segura, Joan, Shao, Chenghua, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., and Burley, Stephen K. Fri . "RCSB Protein Data Bank: Enabling biomedical research and drug discovery". United Kingdom. doi:10.1002/pro.3730.
@article{osti_1576653,
title = {RCSB Protein Data Bank: Enabling biomedical research and drug discovery},
author = {Goodsell, David S. and Zardecki, Christine and Di Costanzo, Luigi and Duarte, Jose M. and Hudson, Brian P. and Persikova, Irina and Segura, Joan and Shao, Chenghua and Voigt, Maria and Westbrook, John D. and Young, Jasmine Y. and Burley, Stephen K.},
abstractNote = {},
doi = {10.1002/pro.3730},
journal = {Protein Science},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on November 28, 2020
Publisher's Version of Record

Save / Share:

Works referenced in this record:

The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints
journal, June 2003

  • Fredriksson, Robert; Lagerström, Malin C.; Lundin, Lars-Gustav
  • Molecular Pharmacology, Vol. 63, Issue 6
  • DOI: 10.1124/mol.63.6.1256

X-ray structure of a voltage-dependent K+ channel
journal, May 2003

  • Jiang, Youxing; Lee, Alice; Chen, Jiayun
  • Nature, Vol. 423, Issue 6935
  • DOI: 10.1038/nature01580

The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology
journal, May 2015


NGL viewer: web-based molecular graphics for large complexes
journal, May 2018


New design strategies for antidepressant drugs
journal, August 2013

  • Immadisetty, Kalyan; Geffert, Laura M.; Surratt, Christopher K.
  • Expert Opinion on Drug Discovery, Vol. 8, Issue 11
  • DOI: 10.1517/17460441.2013.830102

Economic Impacts of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank
journal, May 2017


The Resolution Revolution
journal, March 2014


Structural Models of Ligand-Gated Ion Channels: Sites of Action for Anesthetics and Ethanol
journal, October 2013

  • Olsen, Richard W.; Li, Guo-Dong; Wallner, Martin
  • Alcoholism: Clinical and Experimental Research, Vol. 38, Issue 3
  • DOI: 10.1111/acer.12283

Structures of human Na v 1.7 channel in complex with auxiliary subunits and animal toxins
journal, February 2019


GLP-1 as a target for therapeutic intervention
journal, December 2016


Structure of the human voltage-gated sodium channel Na v 1.4 in complex with β1
journal, September 2018


Plant ubiquitin ligases as signaling hubs
journal, April 2014

  • Shabek, Nitzan; Zheng, Ning
  • Nature Structural & Molecular Biology, Vol. 21, Issue 4
  • DOI: 10.1038/nsmb.2804

Protacs: Chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation
journal, July 2001

  • Sakamoto, K. M.; Kim, K. B.; Kumagai, A.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 15
  • DOI: 10.1073/pnas.141230798

Structure and mechanism of AMPA receptor — auxiliary protein complexes
journal, February 2019


Classics in Chemical Neuroscience: Memantine
journal, July 2017


Modulation of Ligand-gated Ion Channels by Antidepressants and Antipsychotics
journal, September 2007


The ABCs of membrane transporters in health and disease (SLC series): Introduction
journal, April 2013

  • Hediger, Matthias A.; Clémençon, Benjamin; Burrier, Robert E.
  • Molecular Aspects of Medicine, Vol. 34, Issue 2-3
  • DOI: 10.1016/j.mam.2012.12.009

Adhesion G Protein-Coupled Receptors as Drug Targets for Neurological Diseases
journal, April 2019

  • Folts, Christopher J.; Giera, Stefanie; Li, Tao
  • Trends in Pharmacological Sciences, Vol. 40, Issue 4
  • DOI: 10.1016/j.tips.2019.02.003

Overview of Transporters in Pharmacokinetics and Drug Discovery
journal, August 2018

  • Zhang, Yan
  • Current Protocols in Pharmacology, Vol. 82, Issue 1
  • DOI: 10.1002/cpph.46

Structure of a Conjugating Enzyme-Ubiquitin Thiolester Intermediate Reveals a Novel Role for the Ubiquitin Tail
journal, October 2001


GPCR Engineering Yields High-Resolution Structural Insights into  2-Adrenergic Receptor Function
journal, October 2007


Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM
journal, July 2017

  • Roh, Soung-Hun; Hryc, Corey F.; Jeong, Hyun-Hwan
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 31
  • DOI: 10.1073/pnas.1704725114

Analysis of impact metrics for the Protein Data Bank
journal, October 2018

  • Markosian, Christopher; Di Costanzo, Luigi; Sekharan, Monica
  • Scientific Data, Vol. 5, Issue 1
  • DOI: 10.1038/sdata.2018.212

A CFTR Potentiator in Patients with Cystic Fibrosis and the G551D Mutation
journal, November 2011

  • Ramsey, Bonnie W.; Davies, Jane; McElvaney, N. Gerard
  • New England Journal of Medicine, Vol. 365, Issue 18
  • DOI: 10.1056/NEJMoa1105185

Crystallizing membrane proteins using lipidic mesophases
journal, April 2009


Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation
journal, February 2017


Glutamate Receptor Ion Channels: Structure, Regulation, and Function
journal, August 2010

  • Traynelis, Stephen F.; Wollmuth, Lonnie P.; McBain, Chris J.
  • Pharmacological Reviews, Vol. 62, Issue 3
  • DOI: 10.1124/pr.109.002451

Structural basis for the mechanism of ABC transporters
journal, October 2015

  • Beis, Konstantinos
  • Biochemical Society Transactions, Vol. 43, Issue 5
  • DOI: 10.1042/BST20150047

Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex
journal, April 2002

  • Zheng, Ning; Schulman, Brenda A.; Song, Langzhou
  • Nature, Vol. 416, Issue 6882
  • DOI: 10.1038/416703a

An outlook on using serial femtosecond crystallography in drug discovery
journal, May 2019


The emerging complexity of protein ubiquitination
journal, September 2009

  • Komander, David
  • Biochemical Society Transactions, Vol. 37, Issue 5
  • DOI: 10.1042/BST0370937

Voltage-gated sodium channels: structures, functions, and molecular modeling
journal, July 2019


Separation of two different populations of axial organ cells of Asterias rubens by the use of lectins
journal, September 1978


Crystal Structure of the Ligand-bound Glucagon-like Peptide-1 Receptor Extracellular Domain
journal, February 2008

  • Runge, Steffen; Thøgersen, Henning; Madsen, Kjeld
  • Journal of Biological Chemistry, Vol. 283, Issue 17
  • DOI: 10.1074/jbc.M708740200

Utility of protein structures in overcoming ADMET-related issues of drug-like compounds
journal, June 2011


New tools and functions in data-out activities at Protein Data Bank Japan (PDBj): New tools and functions in PDBj data-out
journal, September 2017

  • Kinjo, Akira R.; Bekker, Gert-Jan; Wako, Hiroshi
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3273

Plasticity in binding confers selectivity in ligand-induced protein degradation
journal, June 2018

  • Nowak, Radosław P.; DeAngelo, Stephen L.; Buckley, Dennis
  • Nature Chemical Biology, Vol. 14, Issue 7
  • DOI: 10.1038/s41589-018-0055-y

The Transporter Classification Database (TCDB): recent advances
journal, November 2015

  • Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1103

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Structure and Mechanism of the Lactose Permease of Escherichia coli
journal, August 2003


Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
journal, August 2000


RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1004

Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding
journal, March 2009


Allosteric Modulation of Ionotropic Glutamate Receptors Special Issue
journal, November 2018

  • Carruthers, Nicholas I.; Lovenberg, Timothy W.; Traynelis, Stephen F.
  • ACS Medicinal Chemistry Letters, Vol. 10, Issue 3
  • DOI: 10.1021/acsmedchemlett.9b00047

X-ray structures and mechanism of the human serotonin transporter
journal, April 2016

  • Coleman, Jonathan A.; Green, Evan M.; Gouaux, Eric
  • Nature, Vol. 532, Issue 7599
  • DOI: 10.1038/nature17629

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma
journal, September 2010

  • Bollag, Gideon; Hirth, Peter; Tsai, James
  • Nature, Vol. 467, Issue 7315
  • DOI: 10.1038/nature09454

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
journal, November 2012

  • Velankar, Sameer; Dana, José M.; Jacobsen, Julius
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1258

A complicated complex: Ion channels, voltage sensing, cell membranes and peptide inhibitors
journal, July 2018


An SCN9A channelopathy causes congenital inability to experience pain
journal, December 2006

  • Cox, James J.; Reimann, Frank; Nicholas, Adeline K.
  • Nature, Vol. 444, Issue 7121
  • DOI: 10.1038/nature05413

Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein
journal, May 2017


Cystic fibrosis
journal, November 2016


A primer on the mechanics of P-glycoprotein the multidrug transporter
journal, January 2007


SWISS-MODEL: homology modelling of protein structures and complexes
journal, May 2018

  • Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan
  • Nucleic Acids Research, Vol. 46, Issue W1
  • DOI: 10.1093/nar/gky427

The Protein Data Bank
journal, January 2000


Protein Data Bank: the single global archive for 3D macromolecular structure data
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky949

Structural identification of a hotspot on CFTR for potentiation
journal, June 2019


Ivermectin: uses and impact 20 years on
journal, January 2006


Molecular mechanisms of cereblon-based drugs
journal, October 2019


Structural biology of solute carrier (SLC) membrane transport proteins
journal, February 2017


Ubiquitin Ligases: Structure, Function, and Regulation
journal, June 2017


Structure and mechanism of ABC transporters
journal, February 2015


The Structure of the APPBP1-UBA3-NEDD8-ATP Complex Reveals the Basis for Selective Ubiquitin-like Protein Activation by an E1
journal, December 2003


Potentiating SLC transporter activity: Emerging drug discovery opportunities
journal, July 2017

  • Rives, Marie-Laure; Javitch, Jonathan A.; Wickenden, Alan D.
  • Biochemical Pharmacology, Vol. 135
  • DOI: 10.1016/j.bcp.2017.02.010

X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor
journal, November 2009

  • Sobolevsky, Alexander I.; Rosconi, Michael P.; Gouaux, Eric
  • Nature, Vol. 462, Issue 7274
  • DOI: 10.1038/nature08624

Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography
journal, May 2018


Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters
journal, July 2005

  • Yamashita, Atsuko; Singh, Satinder K.; Kawate, Toshimitsu
  • Nature, Vol. 437, Issue 7056
  • DOI: 10.1038/nature03978

Insights into SCF ubiquitin ligases from the structure of the Skp1–Skp2 complex
journal, November 2000

  • Schulman, Brenda A.; Carrano, Andrea C.; Jeffrey, Philip D.
  • Nature, Vol. 408, Issue 6810
  • DOI: 10.1038/35042620

Glutamate receptors at atomic resolution
journal, March 2006


How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals
journal, February 2019


Targeting Cullin–RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation
journal, April 2015

  • Bulatov, Emil; Ciulli, Alessio
  • Biochemical Journal, Vol. 467, Issue 3
  • DOI: 10.1042/BJ20141450

Refined Structure of the Nicotinic Acetylcholine Receptor at 4Å Resolution
journal, March 2005


Structure-Function of the G Protein–Coupled Receptor Superfamily
journal, January 2013


A Call for Systematic Research on Solute Carriers
journal, July 2015


From Toxins Targeting Ligand Gated Ion Channels to Therapeutic Molecules
journal, March 2011

  • Nasiripourdori, Adak; Taly, Valérie; Grutter, Thomas
  • Toxins, Vol. 3, Issue 3
  • DOI: 10.3390/toxins3030260

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank
journal, February 2017


Dissecting diverse functions of NMDA receptors by structural biology
journal, February 2019


Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State
journal, May 2011


The crystal structure of a voltage-gated sodium channel
journal, July 2011

  • Payandeh, Jian; Scheuer, Todd; Zheng, Ning
  • Nature, Vol. 475, Issue 7356
  • DOI: 10.1038/nature10238

Molecular basis for pore blockade of human Na + channel Na v 1.2 by the μ-conotoxin KIIIA
journal, February 2019


Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis
journal, November 2014


Alternating Access in Maltose Transporter Mediated by Rigid-Body Rotations
journal, February 2009


Crystal structure of a catalytic intermediate of the maltose transporter
journal, November 2007

  • Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A.
  • Nature, Vol. 450, Issue 7169
  • DOI: 10.1038/nature06264

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe
journal, November 2017

  • Mir, Saqib; Alhroub, Younes; Anyango, Stephen
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1070

BioMagResBank
journal, December 2007

  • Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm957

A comprehensive map of molecular drug targets
journal, December 2016

  • Santos, Rita; Ursu, Oleg; Gaulton, Anna
  • Nature Reviews Drug Discovery, Vol. 16, Issue 1
  • DOI: 10.1038/nrd.2016.230

Adhesion G Protein–Coupled Receptors as Drug Targets
journal, January 2018


A nomenclature for ligand-gated ion channels
journal, January 2009


Voltage gated sodium channels as drug discovery targets
journal, July 2015


Functional Insights from Glutamate Receptor Ion Channel Structures
journal, February 2013


Voltage-Gated Sodium Channels: Structure, Function, Pharmacology, and Clinical Indications
journal, May 2015

  • de Lera Ruiz, Manuel; Kraus, Richard L.
  • Journal of Medicinal Chemistry, Vol. 58, Issue 18
  • DOI: 10.1021/jm501981g

Structure of the chemokine receptor CXCR1 in phospholipid bilayers
journal, October 2012

  • Park, Sang Ho; Das, Bibhuti B.; Casagrande, Fabio
  • Nature, Vol. 491, Issue 7426
  • DOI: 10.1038/nature11580

ModBase, a database of annotated comparative protein structure models and associated resources
journal, November 2013

  • Pieper, Ursula; Webb, Benjamin M.; Dong, Guang Qiang
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1144

Structural basis of PROTAC cooperative recognition for selective protein degradation
journal, March 2017

  • Gadd, Morgan S.; Testa, Andrea; Lucas, Xavier
  • Nature Chemical Biology, Vol. 13, Issue 5
  • DOI: 10.1038/nchembio.2329

Discovery of the Once-Weekly Glucagon-Like Peptide-1 (GLP-1) Analogue Semaglutide
journal, September 2015


Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia
journal, March 2004